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Timilsina S, Kaur A, Sharma A, Ramamoorthy S, Vallad GE, Wang N, White FF, Potnis N, Goss EM, Jones JB. Xanthomonas as a Model System for Studying Pathogen Emergence and Evolution. PHYTOPATHOLOGY 2024; 114:1433-1446. [PMID: 38648116 DOI: 10.1094/phyto-03-24-0084-rvw] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
In this review, we highlight studies in which whole-genome sequencing, comparative genomics, and population genomics have provided unprecedented insights into past and ongoing pathogen evolution. These include new understandings of the adaptive evolution of secretion systems and their effectors. We focus on Xanthomonas pathosystems that have seen intensive study and improved our understanding of pathogen emergence and evolution, particularly in the context of host specialization: citrus canker, bacterial blight of rice, and bacterial spot of tomato and pepper. Across pathosystems, pathogens appear to follow a pattern of bursts of evolution and diversification that impact host adaptation. There remains a need for studies on the mechanisms of host range evolution and genetic exchange among closely related but differentially host-specialized species and to start moving beyond the study of specific strain and host cultivar pairwise interactions to thinking about these pathosystems in a community context.
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Affiliation(s)
- Sujan Timilsina
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611
| | - Amandeep Kaur
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611
| | - Anuj Sharma
- Department of Horticultural Sciences, Gulf Coast Research and Education Center, University of Florida, Wimauma, FL 33598
| | | | - Gary E Vallad
- Department of Plant Pathology, Gulf Coast Research and Education Center, University of Florida, Wimauma, FL 33598
| | - Nian Wang
- Department of Microbiology and Cell Science, Citrus Research and Education Center, University of Florida, Lake Alfred, FL 33850
| | - Frank F White
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611
| | - Neha Potnis
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849
| | - Erica M Goss
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32610
| | - Jeffrey B Jones
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611
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Chen JR, Aguirre-Carvajal K, Xue DY, Chang HC, Arone-Maxwell L, Lin YP, Armijos-Jaramillo V, Oliva R. Exploring the genetic makeup of Xanthomonas species causing bacterial spot in Taiwan: evidence of population shift and local adaptation. Front Microbiol 2024; 15:1408885. [PMID: 38846563 PMCID: PMC11153759 DOI: 10.3389/fmicb.2024.1408885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 05/13/2024] [Indexed: 06/09/2024] Open
Abstract
The introduction of plant pathogens can quickly reshape disease dynamics in island agro-ecologies, representing a continuous challenge for local crop management strategies. Xanthomonas pathogens causing tomato bacterial spot were probably introduced in Taiwan several decades ago, creating a unique opportunity to study the genetic makeup and adaptive response of this alien population. We examined the phenotypic and genotypic identity of 669 pathogen entries collected across different regions of Taiwan in the last three decades. The analysis detected a major population shift, where X. euvesicatoria and X. vesicatoria races T1 and T2 were replaced by new races of X. perforans. After its introduction, race T4 quickly became dominant in all tomato-growing areas of the island. The genomic analysis of 317 global genomes indicates that the Xanthomonas population in Taiwan has a narrow genetic background, most likely resulting from a small number of colonization events. However, despite the apparent genetic uniformity, X. perforans race T4 shows multiple phenotypic responses in tomato lines. Additionally, an in-depth analysis of effector composition suggests diversification in response to local adaptation. These include unique mutations on avrXv3 which might allow the pathogen to overcome Xv3/Rx4 resistance gene. The findings underscore the dynamic evolution of a pathogen when introduced in a semi-isolated environment and provide insights into the potential management strategies for this important disease of tomato.
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Affiliation(s)
- Jaw-Rong Chen
- Safe and Sustainable Value Chain, World Vegetable Center, Shanhua, Taiwan
| | - Kevin Aguirre-Carvajal
- Research Center of Information and Communication Technologies, University of A Coruña, A Coruña, Spain
- Bio-Cheminformatics Research Group, Universidad de Las Américas, Quito, Ecuador
| | - Dao-Yuan Xue
- Seed and Seedling Management Section, Taiwan Seed Improvement and Propagation Station, Ministry of Agriculture, Taichung, Taiwan
| | - Hung-Chia Chang
- Safe and Sustainable Value Chain, World Vegetable Center, Shanhua, Taiwan
| | | | - Ya-Ping Lin
- Safe and Sustainable Value Chain, World Vegetable Center, Shanhua, Taiwan
| | - Vinicio Armijos-Jaramillo
- Bio-Cheminformatics Research Group, Universidad de Las Américas, Quito, Ecuador
- Facultad de Ingeniería y Ciencias Aplicadas, Universidad de Las Américas, Quito, Ecuador
| | - Ricardo Oliva
- Safe and Sustainable Value Chain, World Vegetable Center, Shanhua, Taiwan
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Diallo A, Wonni I, Sicard A, Blondin L, Gagnevin L, Vernière C, Szurek B, Hutin M. Genetic Structure and TALome Analysis Highlight a High Level of Diversity in Burkinabe Xanthomonas Oryzae pv. oryzae Populations. RICE (NEW YORK, N.Y.) 2023; 16:33. [PMID: 37523017 PMCID: PMC10390441 DOI: 10.1186/s12284-023-00648-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 07/07/2023] [Indexed: 08/01/2023]
Abstract
Bacterial Leaf Blight of rice (BLB) caused by Xanthomonas oryzae pv. oryzae (Xoo) is a major threat for food security in many rice growing countries including Burkina Faso, where the disease was first reported in the 1980's. In line with the intensification of rice cultivation in West-Africa, BLB incidence has been rising for the last 15 years. West-African strains of Xoo differ from their Asian counterparts as they (i) are genetically distant, (ii) belong to new races and, (iii) contain reduced repertoires of Transcription Activator Like (TAL) effector genes. In order to investigate the evolutionary dynamics of Xoo populations in Burkina Faso, 177 strains were collected from 2003 to 2018 in three regions where BLB is occurring. Multilocus VNTR Analysis (MLVA-14) targeting 10 polymorphic loci discriminated 24 haplotypes and showed that Xoo populations were structured according to their geographical localization and year of collection. Considering their major role in Xoo pathogenicity, we assessed the TAL effector repertoires of the 177 strains upon RFLP-based profiling. Surprisingly, an important diversity was revealed with up to eight different RFLP patterns. Finally, comparing neutral vs. tal effector gene diversity allowed to suggest scenarios underlying the evolutionary dynamics of Xoo populations in Burkina Faso, which is key to rationally guide the deployment of durably resistant rice varieties against BLB in the country.
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Affiliation(s)
- A Diallo
- INERA, Institut de l'Environnement et de Recherches Agricoles du Burkina Faso, Laboratoire de Phytopathologie, Bobo-Dioulasso, Burkina Faso
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - I Wonni
- INERA, Institut de l'Environnement et de Recherches Agricoles du Burkina Faso, Laboratoire de Phytopathologie, Bobo-Dioulasso, Burkina Faso.
| | - A Sicard
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - L Blondin
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - L Gagnevin
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - C Vernière
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - B Szurek
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France.
| | - M Hutin
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
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Song Z, Zheng J, Zhao Y, Yin J, Zheng D, Hu H, Liu H, Sun M, Ruan L, Liu F. Population genomics and pathotypic evaluation of the bacterial leaf blight pathogen of rice reveals rapid evolutionary dynamics of a plant pathogen. Front Cell Infect Microbiol 2023; 13:1183416. [PMID: 37305415 PMCID: PMC10250591 DOI: 10.3389/fcimb.2023.1183416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/05/2023] [Indexed: 06/13/2023] Open
Abstract
The Xanthomonas oryzae pv. oryzae (Xoo) is a bacterial pathogen causing bacterial blight disease in rice, resulting in significant yield reductions of up to 50% in rice production. Despite its serious threat to food production globally, knowledge of its population structure and virulence evolution is relatively limited. In this study, we employed whole-genome sequencing to explore the diversity and evolution of Xoo in the main rice-growing areas of China over the past 30 years. Using phylogenomic analysis, we revealed six lineages. CX-1 and CX-2 primarily contained Xoo isolates from South China, while CX-3 represented Xoo isolates from North China. Xoo isolates belonging to CX-5 and CX-6 were the most prevalent across all studied areas, persisting as dominant lineages for several decades. Recent sporadic disease outbreaks were primarily caused by Xoo isolates derived from the two major lineages, CX-5 and CX-6, although Xoo isolates from other lineages also contributed to these outbreaks. The lineage and sub-lineage distributions of Xoo isolates were strongly correlated with their geographical origin, which was found to be mainly determined by the planting of the two major rice subspecies, indica and japonica. Moreover, large-scale virulence testing was conducted to evaluate the diversity of pathogenicity for Xoo. We found rapid virulence evolution against rice, and its determinant factors included the genetic background of Xoo, rice resistance genes, and planting environment of rice. This study provides an excellent model for understanding the evolution and dynamics of plant pathogens in the context of their interactions with their hosts, which are shaped by a combination of geographical conditions and farming practices. The findings of this study may have important implications for the development of effective strategies for disease management and crop protection in rice production systems.
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Affiliation(s)
- Zhiwei Song
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Jinshui Zheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan, China
| | - Yancun Zhao
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Jiakang Yin
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan, China
| | - Dehong Zheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan, China
| | - Huifeng Hu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan, China
| | - Hongxia Liu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Ming Sun
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan, China
| | - Lifang Ruan
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan, China
| | - Fengquan Liu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
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Teper D, White FF, Wang N. The Dynamic Transcription Activator-Like Effector Family of Xanthomonas. PHYTOPATHOLOGY 2023; 113:651-666. [PMID: 36449529 DOI: 10.1094/phyto-10-22-0365-kd] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Transcription activator-like effectors (TALEs) are bacterial proteins that are injected into the eukaryotic nucleus to act as transcriptional factors and function as key virulence factors of the phytopathogen Xanthomonas. TALEs are translocated into plant host cells via the type III secretion system and induce the expression of host susceptibility (S) genes to facilitate disease. The unique modular DNA binding domains of TALEs comprise an array of nearly identical direct repeats that enable binding to DNA targets based on the recognition of a single nucleotide target per repeat. The very nature of TALE structure and function permits the proliferation of TALE genes and evolutionary adaptations in the host to counter TALE function, making the TALE-host interaction the most dynamic story in effector biology. The TALE genes appear to be a relatively young effector gene family, with a presence in all virulent members of some species and absent in others. Genome sequencing has revealed many TALE genes throughout the xanthomonads, and relatively few have been associated with a cognate S gene. Several species, including Xanthomonas oryzae pv. oryzae and X. citri pv. citri, have near absolute requirement for TALE gene function, while the genes appear to be just now entering the disease interactions with new fitness contributions to the pathogens of tomato and pepper among others. Deciphering the simple and effective DNA binding mechanism also has led to the development of DNA manipulation tools in fields of gene editing and transgenic research. In the three decades since their discovery, TALE research remains at the forefront of the study of bacterial evolution, plant-pathogen interactions, and synthetic biology. We also discuss critical questions that remain to be addressed regarding TALEs.
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Affiliation(s)
- Doron Teper
- Department of Plant Pathology and Weed Research, Agricultural Research Organization, Volcani Institute, Rishon LeZion, Israel
| | - Frank F White
- Department of Plant Pathology, Institute of Food and Agricultural Sciences (IFAS), University of Florida, Gainesville, FL, U.S.A
| | - Nian Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, IFAS, University of Florida, Lake Alfred, FL, U.S.A
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Hou Y, Liang Y, Yang C, Ji Z, Zeng Y, Li G, E Z. Complete Genomic Sequence of Xanthomonas oryzae pv. oryzae Strain, LA20, for Studying Resurgence of Rice Bacterial Blight in the Yangtze River Region, China. Int J Mol Sci 2023; 24:ijms24098132. [PMID: 37175839 PMCID: PMC10179132 DOI: 10.3390/ijms24098132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/25/2023] [Accepted: 04/28/2023] [Indexed: 05/15/2023] Open
Abstract
Xanthomonas oryzae pv. oryzae (Xoo) is a causative agent of rice bacterial blight (BB). In 2020-2022, BB re-emerged, and there was a break out in the Yangtze River area, China. The pandemic Xoo strain, LA20, was isolated and identified from cultivar Quanyou1606 and demonstrated to be the Chinese R9 Xoo strain, which is able to override the widely adopted xa5-, Xa7- and xa13-mediated resistance in rice varieties in Yangtze River. Here, we report the complete genome of LA20 by PacBio and Illumina sequencing. The assembled genome consists of one circular chromosome of 4,960,087 bp, sharing 99.65% sequence identity with the traditional representative strain, YC11 (R5), in the Yangtze River. Comparative genome analysis of LA20 and YC11 revealed the obvious variability in Tal genes (the uppermost virulence determinants) in numbers and sequences. Particularly, six Tal genes were only found in LA20, but not in YC11, among which Tal1b (pthXo1)/Tal4 (pthXo6), along with the lost one, pthXo3 (avrXa7), might be the major factors for LA20 to overcome xa5-, Xa7- and xa13-mediated resistance, thus, leading to the resurgence of BB. This complete genome of the new pandemic Xoo strain will provide novel insights into pathogen evolution, the traits of pathogenicity on genomic level and the epidemic disease status in China.
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Affiliation(s)
- Yuxuan Hou
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China
| | - Yan Liang
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China
| | - Changdeng Yang
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China
| | - Zhijuan Ji
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China
| | - Yuxiang Zeng
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China
| | - Guanghao Li
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China
| | - Zhiguo E
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China
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Li T, Li Y, Ma X, Dan X, Huang X, Li Q, Lei S, Zhang Z, Huang S, Jiang W, Yu Y, He YQ. Comparative Genomic Analysis of Two Xanthomonas oryzae pv. oryzae Strains Isolated From Low Land and High Mountain Paddies in Guangxi, China. Front Microbiol 2022; 13:867633. [PMID: 35572630 PMCID: PMC9096941 DOI: 10.3389/fmicb.2022.867633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 03/15/2022] [Indexed: 11/22/2022] Open
Abstract
Xanthomonas oryzae pv. textitoryzae (Xoo) is a causal agent of rice bacterial leaf blight (BLB), the major rice disease, which is seriously constraining rice production in Asia. The interaction between Xoo and rice is in a dynamic process, essentially the co-evolution. Tracking the occurrence of plant diseases and identifying the epidemic pathogens in time are critical to assessing the epidemic disease status and understanding the pathogen evolution. In 2020, the occurrences of rice BLB were spotted in many places of Guangxi, the major rice growing region in China. Two of the 2020-epidemic Xoo strains, namely, GXO20-01 and GXO20-06, were isolated from low land and high mountain paddies in Guangxi, respectively, and were demonstrated to be race R8 of Chinese Xoo strains, but with significantly different virulence on certain susceptible varieties of rice. The HiFi PacBio sequencing revealed that GXO20-01 and GXO20-06 share the highly syntenic genome structures and the major genome contents, but only differ in <10 genes, including one gene encoding for transcription activator-like effector (TALE). A phylogenomic analysis grouped GXO20-01 and GXO20-06 into the PX-A lineage, stood close to PXO563 and PXO71 strains, but stood away from the other Chinese Xoo strains; for example, the JL25 and YC11. A comparative genomic analysis revealed that the major pathogenicity/virulence genes are conserved in two, newly isolated Xoo strains and the other Xoo strains in PX-A lineage, including the majority genes for the TALomes. The genomic differences between the Xoo strains were pinpointed to a few tal genes, which were variable in both their numbers and sequences, even between GXO20-01 and GXO20-06, the two 2020-epidemic Xoo strains. The study further revealed the instability and variability of tal genes in Xoo and highlighted the utility of HiFi long-read sequencing in TALE analysis and pathogen tracking.
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Affiliation(s)
- Tianjiao Li
- College of Agriculture, Guangxi University, Nanning, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource and College of Life Science and Technology, Nanning, China
| | - Yiming Li
- College of Agriculture, Guangxi University, Nanning, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource and College of Life Science and Technology, Nanning, China
| | - Xiuguo Ma
- College of Agriculture, Guangxi University, Nanning, China
| | - Xue Dan
- College of Agriculture, Guangxi University, Nanning, China
| | - Xianjiao Huang
- College of Agriculture, Guangxi University, Nanning, China
| | - Qinying Li
- Napo Agricultural and Rural Bureau, Napo County, Baise, China
| | - Shimin Lei
- College of Agriculture, Guangxi University, Nanning, China
| | - Zhengchun Zhang
- New Rural Development Institute of Guangxi University, Nanning, China
| | - Sheng Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource and College of Life Science and Technology, Nanning, China
| | - Wei Jiang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource and College of Life Science and Technology, Nanning, China
| | - Yanhua Yu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource and College of Life Science and Technology, Nanning, China
| | - Yong-Qiang He
- College of Agriculture, Guangxi University, Nanning, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresource and College of Life Science and Technology, Nanning, China
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Erkes A, Mücke S, Reschke M, Boch J, Grau J. Epigenetic features improve TALE target prediction. BMC Genomics 2021; 22:914. [PMID: 34965853 PMCID: PMC8717664 DOI: 10.1186/s12864-021-08210-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 11/25/2021] [Indexed: 11/20/2022] Open
Abstract
Background The yield of many crop plants can be substantially reduced by plant-pathogenic Xanthomonas bacteria. The infection strategy of many Xanthomonas strains is based on transcription activator-like effectors (TALEs), which are secreted into the host cells and act as transcriptional activators of plant genes that are beneficial for the bacteria.The modular DNA binding domain of TALEs contains tandem repeats, each comprising two hyper-variable amino acids. These repeat-variable diresidues (RVDs) bind to their target box and determine the specificity of a TALE.All available tools for the prediction of TALE targets within the host plant suffer from many false positives. In this paper we propose a strategy to improve prediction accuracy by considering the epigenetic state of the host plant genome in the region of the target box. Results To this end, we extend our previously published tool PrediTALE by considering two epigenetic features: (i) chromatin accessibility of potentially bound regions and (ii) DNA methylation of cytosines within target boxes. Here, we determine the epigenetic features from publicly available DNase-seq, ATAC-seq, and WGBS data in rice.We benchmark the utility of both epigenetic features separately and in combination, deriving ground-truth from RNA-seq data of infections studies in rice. We find an improvement for each individual epigenetic feature, but especially the combination of both.Having established an advantage in TALE target predicting considering epigenetic features, we use these data for promoterome and genome-wide scans by our new tool EpiTALE, leading to several novel putative virulence targets. Conclusions Our results suggest that it would be worthwhile to collect condition-specific chromatin accessibility data and methylation information when studying putative virulence targets of Xanthomonas TALEs. Supplementary Information The online version contains supplementary material available at (10.1186/s12864-021-08210-z).
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Affiliation(s)
- Annett Erkes
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle, Germany.
| | - Stefanie Mücke
- Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
| | - Maik Reschke
- Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
| | - Jens Boch
- Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
| | - Jan Grau
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle, Germany.
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Zhang F, Hu Z, Wu Z, Lu J, Shi Y, Xu J, Wang X, Wang J, Zhang F, Wang M, Shi X, Cui Y, Vera Cruz C, Zhuo D, Hu D, Li M, Wang W, Zhao X, Zheng T, Fu B, Ali J, Zhou Y, Li Z. Reciprocal adaptation of rice and Xanthomonas oryzae pv. oryzae: cross-species 2D GWAS reveals the underlying genetics. THE PLANT CELL 2021; 33:2538-2561. [PMID: 34467412 PMCID: PMC8408478 DOI: 10.1093/plcell/koab146] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 05/15/2021] [Indexed: 05/23/2023]
Abstract
A 1D/2D genome-wide association study strategy was adopted to investigate the genetic systems underlying the reciprocal adaptation of rice (Oryza sativa) and its bacterial pathogen, Xanthomonas oryzae pv. oryzae (Xoo) using the whole-genome sequencing and large-scale phenotyping data of 701 rice accessions and 23 diverse Xoo strains. Forty-seven Xoo virulence-related genes and 318 rice quantitative resistance genes (QR-genes) mainly located in 41 genomic regions, and genome-wide interactions between the detected virulence-related genes and QR genes were identified, including well-known resistance genes/virulence genes plus many previously uncharacterized ones. The relationship between rice and Xoo was characterized by strong differentiation among Xoo races corresponding to the subspecific differentiation of rice, by strong shifts toward increased resistance/virulence of rice/Xoo populations and by rich genetic diversity at the detected rice QR-genes and Xoo virulence genes, and by genome-wide interactions between many rice QR-genes and Xoo virulence genes in a multiple-to-multiple manner, presumably resulting either from direct protein-protein interactions or from genetic epistasis. The observed complex genetic interaction system between rice and Xoo likely exists in other crop-pathogen systems that would maintain high levels of diversity at their QR-loci/virulence-loci, resulting in dynamic coevolutionary consequences during their reciprocal adaptation.
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Affiliation(s)
- Fan Zhang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Haidian District, Beijing 100081, China
- College of Agronomy, Anhui Agricultural University, 130 West Chang-Jiang Street, Hefei 230036, China
| | - Zhiqiang Hu
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Haidian District, Beijing 100081, China
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
| | - Zhichao Wu
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Haidian District, Beijing 100081, China
| | - Jialing Lu
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Haidian District, Beijing 100081, China
| | - Yingyao Shi
- College of Agronomy, Anhui Agricultural University, 130 West Chang-Jiang Street, Hefei 230036, China
| | - Jianlong Xu
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Haidian District, Beijing 100081, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Xiyin Wang
- School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063009, China
| | - Jinpeng Wang
- School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063009, China
| | - Fan Zhang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Haidian District, Beijing 100081, China
| | - Mingming Wang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Haidian District, Beijing 100081, China
| | - Xiaorong Shi
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Haidian District, Beijing 100081, China
- College of Agronomy, Anhui Agricultural University, 130 West Chang-Jiang Street, Hefei 230036, China
| | - Yanru Cui
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Haidian District, Beijing 100081, China
| | - Casiana Vera Cruz
- International Rice Research Institute, DAPO Box 7777, Metro Manila, The Philippines
| | - Dalong Zhuo
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Haidian District, Beijing 100081, China
- College of Agronomy, Anhui Agricultural University, 130 West Chang-Jiang Street, Hefei 230036, China
| | - Dandan Hu
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Haidian District, Beijing 100081, China
- College of Agronomy, Anhui Agricultural University, 130 West Chang-Jiang Street, Hefei 230036, China
| | - Min Li
- College of Agronomy, Anhui Agricultural University, 130 West Chang-Jiang Street, Hefei 230036, China
| | - Wensheng Wang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Haidian District, Beijing 100081, China
| | - Xiuqin Zhao
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Haidian District, Beijing 100081, China
| | - Tianqing Zheng
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Haidian District, Beijing 100081, China
| | - Binying Fu
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Haidian District, Beijing 100081, China
| | - Jauhar Ali
- International Rice Research Institute, DAPO Box 7777, Metro Manila, The Philippines
| | - Yongli Zhou
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Haidian District, Beijing 100081, China
| | - Zhikang Li
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Haidian District, Beijing 100081, China
- College of Agronomy, Anhui Agricultural University, 130 West Chang-Jiang Street, Hefei 230036, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
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10
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Martel A, Ruiz-Bedoya T, Breit-McNally C, Laflamme B, Desveaux D, Guttman DS. The ETS-ETI cycle: evolutionary processes and metapopulation dynamics driving the diversification of pathogen effectors and host immune factors. CURRENT OPINION IN PLANT BIOLOGY 2021; 62:102011. [PMID: 33677388 DOI: 10.1016/j.pbi.2021.102011] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/21/2021] [Accepted: 01/24/2021] [Indexed: 05/13/2023]
Abstract
The natural diversity of pathogen effectors and host immune components represents a snapshot of the underlying evolutionary processes driving the host-pathogen arms race. In plants, this arms race is manifested by an ongoing cycle of disease and resistance driven by pathogenic effectors that promote disease (effector-triggered susceptibility; ETS) and plant resistance proteins that recognize effector activity to trigger immunity (effector-triggered immunity; ETI). Here we discuss how this ongoing ETS-ETI cycle has shaped the natural diversity of both plant resistance proteins and pathogen effectors. We focus on the evolutionary forces that drive the diversification of the molecules that determine the outcome of plant-pathogen interactions and introduce the concept of metapopulation dynamics (i.e., the introduction of genetic variation from conspecific organisms in different populations) as an alternative mechanism that can introduce and maintain diversity in both host and pathogen populations.
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Affiliation(s)
- Alexandre Martel
- Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario M6S2Y1, Canada
| | - Tatiana Ruiz-Bedoya
- Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario M6S2Y1, Canada
| | - Clare Breit-McNally
- Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario M6S2Y1, Canada
| | - Bradley Laflamme
- Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario M6S2Y1, Canada
| | - Darrell Desveaux
- Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario M6S2Y1, Canada; Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, Ontario M6S2Y1, Canada.
| | - David S Guttman
- Department of Cell & Systems Biology, University of Toronto, Toronto, Ontario M6S2Y1, Canada; Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, Ontario M6S2Y1, Canada.
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11
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Fernandes C, Martins L, Teixeira M, Blom J, Pothier JF, Fonseca NA, Tavares F. Comparative Genomics of Xanthomonas euroxanthea and Xanthomonas arboricola pv. juglandis Strains Isolated from a Single Walnut Host Tree. Microorganisms 2021; 9:microorganisms9030624. [PMID: 33803052 PMCID: PMC8003016 DOI: 10.3390/microorganisms9030624] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/12/2021] [Accepted: 03/15/2021] [Indexed: 11/20/2022] Open
Abstract
The recent report of distinct Xanthomonas lineages of Xanthomonas arboricola pv. juglandis and Xanthomonas euroxanthea within the same walnut tree revealed that this consortium of walnut-associated Xanthomonas includes both pathogenic and nonpathogenic strains. As the implications of this co-colonization are still poorly understood, in order to unveil niche-specific adaptations, the genomes of three X. euroxanthea strains (CPBF 367, CPBF 424T, and CPBF 426) and of an X. arboricola pv. juglandis strain (CPBF 427) isolated from a single walnut tree in Loures (Portugal) were sequenced with two different technologies, Illumina and Nanopore, to provide consistent single scaffold chromosomal sequences. General genomic features showed that CPBF 427 has a genome similar to other X. arboricola pv. juglandis strains, regarding its size, number, and content of CDSs, while X. euroxanthea strains show a reduction regarding these features comparatively to X. arboricola pv. juglandis strains. Whole genome comparisons revealed remarkable genomic differences between X. arboricola pv. juglandis and X. euroxanthea strains, which translates into different pathogenicity and virulence features, namely regarding type 3 secretion system and its effectors and other secretory systems, chemotaxis-related proteins, and extracellular enzymes. Altogether, the distinct genomic repertoire of X. euroxanthea may be particularly useful to address pathogenicity emergence and evolution in walnut-associated Xanthomonas.
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Affiliation(s)
- Camila Fernandes
- CIBIO—Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO-Laboratório Associado, Universidade do Porto, Rua Padre Armando Quintas 7, 4485-661 Vairão, Portugal; (L.M.); (M.T.); (N.A.F.)
- FCUP—Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
- Unidade Estratégica de Investigação e Serviços de Sistemas Agrários e Florestais e Sanidade Vegetal, INIAV, Avenida da República, Quinta do Marquês, 2780-157 Oeiras, Portugal
- Correspondence: (C.F.); (F.T.)
| | - Leonor Martins
- CIBIO—Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO-Laboratório Associado, Universidade do Porto, Rua Padre Armando Quintas 7, 4485-661 Vairão, Portugal; (L.M.); (M.T.); (N.A.F.)
- FCUP—Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Miguel Teixeira
- CIBIO—Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO-Laboratório Associado, Universidade do Porto, Rua Padre Armando Quintas 7, 4485-661 Vairão, Portugal; (L.M.); (M.T.); (N.A.F.)
- FCUP—Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig University Giessen, Ludwigstraße 23, 35390 Giessen, Germany;
| | - Joël F. Pothier
- Environmental Genomics and Systems Biology Research Group, Institute for Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), Einsiedlerstrasse 31, 8820 Wädenswil, Switzerland;
| | - Nuno A. Fonseca
- CIBIO—Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO-Laboratório Associado, Universidade do Porto, Rua Padre Armando Quintas 7, 4485-661 Vairão, Portugal; (L.M.); (M.T.); (N.A.F.)
| | - Fernando Tavares
- CIBIO—Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO-Laboratório Associado, Universidade do Porto, Rua Padre Armando Quintas 7, 4485-661 Vairão, Portugal; (L.M.); (M.T.); (N.A.F.)
- FCUP—Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
- Correspondence: (C.F.); (F.T.)
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12
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Duan G, Bao J, Chen X, Xie J, Liu Y, Chen H, Zheng H, Tang W, Wang Z. Large-Scale Genome Scanning within Exonic Regions Revealed the Contributions of Selective Sweep Prone Genes to Host Divergence and Adaptation in Magnaporthe oryzae Species Complex. Microorganisms 2021; 9:562. [PMID: 33803140 PMCID: PMC8000120 DOI: 10.3390/microorganisms9030562] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/05/2021] [Accepted: 03/06/2021] [Indexed: 11/30/2022] Open
Abstract
Magnaporthe oryzae, one of the most notorious plant pathogens in the agronomic ecosystem, causes a destructive rice blast disease around the world. The blast fungus infects wide arrays of cultivated and non-cultivated plants within the Poaceae. Studies have shown that host speciation exerts selection pressure that drives the evolution and divergence of the M. oryzae population. Population genetic relationship deducted by genome-wide single nucleotide polymorphisms showed that M. oryzae differentiation is highly consistent with the host speciation process. In particular, the rice-infecting population of M. oryzae is distinct from populations from other hosts. However, how genome regions prone to host-mediated selection pressures associated with speciation in M. oryzae, especially at a large-scale population level, has not been extensively characterized. Here, we detected strong evidence of sweep selection throughout the genomes of rice and non-rice pathotypes of M. oryzae population using integrated haplotype score (iHS), cross population extended haplotype homozygosity (XPEHH), and cross population composite likelihood ratio (XPCLR) tests. Functional annotation analyses of the genes associated with host-mediated selection pressure showed that 14 pathogenicity-related genes are under positive selection pressure. Additionally, we showed that 17 candidate effector proteins are under positive and divergent selection among the blast fungus population through sweep selection analysis. Specifically, we find that a divergent selective gene, MGG_13871, is experiencing host-directed mutation in two amino acid residues in rice and non-rice infecting populations. These results provide a crucial insight into the impact of selective sweeping on the differentiation of M. oryzae populations and the dynamic influences of genomic regions in promoting host adaptation and speciation among M. oryzae species.
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Affiliation(s)
- Guohua Duan
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, The School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (G.D.); (J.B.); (X.C.); (J.X.); (Y.L.); (H.C.); (H.Z.)
- Fujian Universities Key Laboratory for Plant-Microbe Interaction, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jiandong Bao
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, The School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (G.D.); (J.B.); (X.C.); (J.X.); (Y.L.); (H.C.); (H.Z.)
| | - Xiaomin Chen
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, The School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (G.D.); (J.B.); (X.C.); (J.X.); (Y.L.); (H.C.); (H.Z.)
- Fujian Universities Key Laboratory for Plant-Microbe Interaction, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jiahui Xie
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, The School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (G.D.); (J.B.); (X.C.); (J.X.); (Y.L.); (H.C.); (H.Z.)
- Fujian Universities Key Laboratory for Plant-Microbe Interaction, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuchan Liu
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, The School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (G.D.); (J.B.); (X.C.); (J.X.); (Y.L.); (H.C.); (H.Z.)
| | - Huiquan Chen
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, The School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (G.D.); (J.B.); (X.C.); (J.X.); (Y.L.); (H.C.); (H.Z.)
- Fuzhou Institute of Oceanography, Minjiang University, Fuzhou 350108, China
| | - Huakun Zheng
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, The School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (G.D.); (J.B.); (X.C.); (J.X.); (Y.L.); (H.C.); (H.Z.)
- Fujian Universities Key Laboratory for Plant-Microbe Interaction, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wei Tang
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, The School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (G.D.); (J.B.); (X.C.); (J.X.); (Y.L.); (H.C.); (H.Z.)
- Fujian Universities Key Laboratory for Plant-Microbe Interaction, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zonghua Wang
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, The School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (G.D.); (J.B.); (X.C.); (J.X.); (Y.L.); (H.C.); (H.Z.)
- Fujian Universities Key Laboratory for Plant-Microbe Interaction, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fuzhou Institute of Oceanography, Minjiang University, Fuzhou 350108, China
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13
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Huerta AI, Delorean EE, Bossa‐Castro AM, Tonnessen BW, Raghavan C, Corral R, Pérez‐Quintero ÁL, Leung H, Verdier V, Leach JE. Resistance and susceptibility QTL identified in a rice MAGIC population by screening with a minor-effect virulence factor from Xanthomonas oryzae pv. oryzae. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:51-63. [PMID: 32594636 PMCID: PMC7769240 DOI: 10.1111/pbi.13438] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 06/02/2020] [Accepted: 06/17/2020] [Indexed: 05/07/2023]
Abstract
Effective and durable disease resistance for bacterial blight (BB) of rice is a continuous challenge due to the evolution and adaptation of the pathogen, Xanthomonas oryzae pv. oryzae (Xoo), on cultivated rice varieties. Fundamental to this pathogens' virulence is transcription activator-like (TAL) effectors that activate transcription of host genes and contribute differently to pathogen virulence, fitness or both. Host plant resistance is predicted to be more durable if directed at strategic virulence factors that impact both pathogen virulence and fitness. We characterized Tal7b, a minor-effect virulence factor that contributes incrementally to pathogen virulence in rice, is a fitness factor to the pathogen and is widely present in geographically diverse strains of Xoo. To identify sources of resistance to this conserved effector, we used a highly virulent strain carrying a plasmid borne copy of Tal7b to screen an indica multi-parent advanced generation inter-cross (MAGIC) population. Of 18 QTL revealed by genome-wide association studies and interval mapping analysis, six were specific to Tal7b (qBB-tal7b). Overall, 150 predicted Tal7b gene targets overlapped with qBB-tal7b QTL. Of these, 21 showed polymorphisms in the predicted effector binding element (EBE) site and 23 lost the EBE sequence altogether. Inoculation and bioinformatics studies suggest that the Tal7b target in one of the Tal7b-specific QTL, qBB-tal7b-8, is a disease susceptibility gene and that the resistance mechanism for this locus may be through loss of susceptibility. Our work demonstrates that minor-effect virulence factors significantly contribute to disease and provide a potential new approach to identify effective disease resistance.
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Affiliation(s)
- Alejandra I. Huerta
- Department of Agricultural BiologyColorado State UniversityFort CollinsCOUSA
- Present address:
Department of Entomology and Plant PathologyNorth Carolina State UniversityRaleighNCUSA
| | - Emily E. Delorean
- Department of Agricultural BiologyColorado State UniversityFort CollinsCOUSA
- Present address:
Department of Plant PathologyKansas State UniversityManhattanKS66506USA
| | - Ana M. Bossa‐Castro
- Department of Agricultural BiologyColorado State UniversityFort CollinsCOUSA
| | - Bradley W. Tonnessen
- Department of Agricultural BiologyColorado State UniversityFort CollinsCOUSA
- Present address:
Extension Plant SciencesNew Mexico State UniversityLas CrucesNM88003USA
| | - Chitra Raghavan
- Division Genetics and BiotechnologyInternational Rice Research InstituteManilaPhilippines
- Present address:
Queensland Department of Agriculture and FisheriesHorticulture and Forestry SciencesCairnsQLD4870Australia
| | - Rene Corral
- Department of Agricultural BiologyColorado State UniversityFort CollinsCOUSA
| | | | - Hei Leung
- Division Genetics and BiotechnologyInternational Rice Research InstituteManilaPhilippines
| | | | - Jan E. Leach
- Department of Agricultural BiologyColorado State UniversityFort CollinsCOUSA
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14
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Carpenter SCD, Mishra P, Ghoshal C, Dash PK, Wang L, Midha S, Laha GS, Lore JS, Kositratana W, Singh NK, Singh K, Patil PB, Oliva R, Patarapuwadol S, Bogdanove AJ, Rai R. An xa5 Resistance Gene-Breaking Indian Strain of the Rice Bacterial Blight Pathogen Xanthomonas oryzae pv. oryzae Is Nearly Identical to a Thai Strain. Front Microbiol 2020; 11:579504. [PMID: 33193207 PMCID: PMC7610140 DOI: 10.3389/fmicb.2020.579504] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 08/31/2020] [Indexed: 11/16/2022] Open
Abstract
The rice bacterial blight pathogen Xanthomonas oryzae pv. oryzae (Xoo) constrains production in major rice growing countries of Asia. Xoo injects transcription activator-like effectors (TALEs) that bind to and activate host “susceptibility” (S) genes that are important for disease. The bacterial blight resistance gene xa5, which reduces TALE activity generally, has been widely deployed. However, strains defeating xa5 have been reported in India and recently also in Thailand. We completely sequenced and compared the genomes of one such strain from each country and examined the encoded TALEs. The two genomes are nearly identical, including the TALE genes, and belong to a previously identified, highly clonal lineage. Each strain harbors a TALE known to activate the major S gene SWEET11 strongly enough to be effective even when diminished by xa5. The findings suggest international migration of the xa5-compatible pathotype and highlight the utility of whole genome sequencing and TALE analysis for understanding and responding to breakdown of resistance.
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Affiliation(s)
- Sara C D Carpenter
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Prashant Mishra
- Plant Pathogen Interaction, ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | - Chandrika Ghoshal
- Plant Pathogen Interaction, ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | - Prasanta K Dash
- Plant Pathogen Interaction, ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | - Li Wang
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Samriti Midha
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Gouri S Laha
- Department of Plant Pathology, ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - Jagjeet S Lore
- Department of Plant Pathology, Punjab Agricultural University, Ludhiana, India
| | - Wichai Kositratana
- Department of Plant Pathology, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom, Thailand
| | - Nagendra K Singh
- Plant Pathogen Interaction, ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | - Kuldeep Singh
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Prabhu B Patil
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Ricardo Oliva
- Rice Breeding Platform, International Rice Research Institute, Los Banos, Philippines
| | - Sujin Patarapuwadol
- Department of Plant Pathology, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom, Thailand
| | - Adam J Bogdanove
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Rhitu Rai
- Plant Pathogen Interaction, ICAR-National Institute for Plant Biotechnology, New Delhi, India
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15
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Sakthivel K, Kumar A, Gautam RK, Manigundan K, Laha GS, Velazhahan R, Singh R, Yadav IS. Intra-regional diversity of rice bacterial blight pathogen, Xanthomonas oryzae pv. oryzae, in the Andaman Islands, India: revelation by pathotyping and multilocus sequence typing. J Appl Microbiol 2020; 130:1259-1272. [PMID: 32767623 DOI: 10.1111/jam.14813] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 07/03/2020] [Accepted: 07/28/2020] [Indexed: 02/06/2023]
Abstract
AIM To investigate the genetic and pathogenic variability of Xanthomonas oryzae pv. oryzae causing bacterial blight in rice on the remote Andaman Islands, India. METHODS AND RESULTS A total of 27 yellow-pigmented bacterial isolates representing rice fields of Andaman Islands incited blight on the susceptible-rice cultivar, C14-8. Phenotypic, pathogenic traits and 16S rRNA gene sequences revealed their identity as X. oryzae pv. oryzae. Virulence profiling indicated the prevalence of seven pathotypes of X. oryzae pv. oryzae on the Islands. Pathotypes-VI and -VII were highly virulent, whereas the pathotype-I was less virulent. Multilocus sequence typing based on nucleotide sequence polymorphism in nine housekeeping genes dnaK; fyuA; gyrB (two loci): rpoD; fusA; gapA; gltA and lepA clustered 27 isolates into 17 sequence types (STs) segregated into two clonal-complexes (CC). While CC-I comprised of isolates from Andaman Island, the CC-II is a mixture of isolates representing mainland India and Andaman Island. The data revealed trans-boundary pathogen introduction and a consequent intra-regional diversification on these islands due to the deployment of different rice cultivars in different regions. CONCLUSIONS Genotyping and pathotyping of sland isolates revealed seven pathotypes distributed in two clonal complexes with strong indications for trans-boundary movement and consequent diversification of the bacterial pathogen. Highly virulent pathotypes of X. oryzae pv. oryzae that could overcome combinations of R-genes, xa13+Xa21 as well as xa5+xa13 were found prevalent in the Andaman Islands SIGNIFICANCE AND IMPACT OF THE STUDY: Genetic and virulence analysis of X. oryzae pv. oryzae in the Andaman Islands revealed introduction and host-mediated regional diversification and local adaptation of X oryzae pv. oryzae. The study calls for the need of multi-gene pyramiding for durable disease resistance and establishing stringent quarantine measures for safeguarding island agricultural practices in the future.
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Affiliation(s)
- K Sakthivel
- Division of Field Crop Improvement and Protection, ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, India
| | - A Kumar
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - R K Gautam
- Division of Field Crop Improvement and Protection, ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, India
| | - K Manigundan
- Division of Field Crop Improvement and Protection, ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, India
| | - G S Laha
- Division of Crop Protection, ICAR-Indian Institute of Rice Research, Hyderabad, Telangana, India
| | - R Velazhahan
- Center for Plant Protection Studies, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - R Singh
- Division of Field Crop Improvement and Protection, ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, India
| | - I S Yadav
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, India
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16
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Gene Pyramiding for Sustainable Crop Improvement against Biotic and Abiotic Stresses. AGRONOMY-BASEL 2020. [DOI: 10.3390/agronomy10091255] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Sustainable agricultural production is endangered by several ecological factors, such as drought, extreme temperatures, excessive salts, parasitic ailments, and insect pest infestation. These challenging environmental factors may have adverse effects on future agriculture production in many countries. In modern agriculture, conventional crop-breeding techniques alone are inadequate for achieving the increasing population’s food demand on a sustainable basis. The advancement of molecular genetics and related technologies are promising tools for the selection of new crop species. Gene pyramiding through marker-assisted selection (MAS) and other techniques have accelerated the development of durable resistant/tolerant lines with high accuracy in the shortest period of time for agricultural sustainability. Gene stacking has not been fully utilized for biotic stress resistance development and quality improvement in most of the major cultivated crops. This review emphasizes on gene pyramiding techniques that are being successfully deployed in modern agriculture for improving crop tolerance to biotic and abiotic stresses for sustainable crop improvement.
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17
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Timilsina S, Potnis N, Newberry EA, Liyanapathiranage P, Iruegas-Bocardo F, White FF, Goss EM, Jones JB. Xanthomonas diversity, virulence and plant-pathogen interactions. Nat Rev Microbiol 2020; 18:415-427. [PMID: 32346148 DOI: 10.1038/s41579-020-0361-8] [Citation(s) in RCA: 132] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/19/2020] [Indexed: 12/19/2022]
Abstract
Xanthomonas spp. encompass a wide range of plant pathogens that use numerous virulence factors for pathogenicity and fitness in plant hosts. In this Review, we examine recent insights into host-pathogen co-evolution, diversity in Xanthomonas populations and host specificity of Xanthomonas spp. that have substantially improved our fundamental understanding of pathogen biology. We emphasize the virulence factors in xanthomonads, such as type III secreted effectors including transcription activator-like effectors, type II secretion systems, diversity resulting in host specificity, evolution of emerging strains, activation of susceptibility genes and strategies of host evasion. We summarize the genomic diversity in several Xanthomonas spp. and implications for disease outbreaks, management strategies and breeding for disease resistance.
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Affiliation(s)
- Sujan Timilsina
- Plant Pathology Department, University of Florida, Gainesville, FL, USA
| | - Neha Potnis
- Entomology and Plant Pathology, Auburn University, Auburn, AL, USA
| | - Eric A Newberry
- Entomology and Plant Pathology, Auburn University, Auburn, AL, USA
| | | | | | - Frank F White
- Plant Pathology Department, University of Florida, Gainesville, FL, USA
| | - Erica M Goss
- Plant Pathology Department, University of Florida, Gainesville, FL, USA. .,Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA.
| | - Jeffrey B Jones
- Plant Pathology Department, University of Florida, Gainesville, FL, USA.
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18
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Haq F, Xie S, Huang K, Shah SMA, Ma W, Cai L, Xu X, Xu Z, Wang S, Zou L, Zhu B, Chen G. Identification of a virulence tal gene in the cotton pathogen, Xanthomonas citri pv. malvacearum strain Xss-V 2-18. BMC Microbiol 2020; 20:91. [PMID: 32293266 PMCID: PMC7160923 DOI: 10.1186/s12866-020-01783-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 04/05/2020] [Indexed: 01/22/2023] Open
Abstract
Background Bacterial blight of cotton (BBC), which is caused by the bacterium Xanthomonas citri pv. malvacearum (Xcm), is a destructive disease in cotton. Transcription activator-like effectors (TALEs), encoded by tal-genes, play critical roles in the pathogenesis of xanthomonads. Characterized strains of cotton pathogenic Xcm harbor 8–12 different tal genes and only one of them is functionally decoded. Further identification of novel tal genes in Xcm strains with virulence contributions are prerequisite to decipher the Xcm-cotton interactions. Results In this study, we identified six tal genes in Xss-V2–18, a highly-virulent strain of Xcm from China, and assessed their role in BBC. RFLP-based Southern hybridization assays indicated that Xss-V2–18 harbors the six tal genes on a plasmid. The plasmid-encoded tal genes were isolated by cloning BamHI fragments and screening clones by colony hybridization. The tal genes were sequenced by inserting a Tn5 transposon in the DNA encoding the central repeat region (CRR) of each tal gene. Xcm TALome evolutionary relationship based on TALEs CRR revealed relatedness of Xss-V2–18 to MSCT1 and MS14003 from the United States. However, Tal2 of Xss-V2–18 differs at two repeat variable diresidues (RVDs) from Tal6 and Tal26 in MSCT1 and MS14003, respectively, inferred functional dissimilarity. The suicide vector pKMS1 was then used to construct tal deletion mutants in Xcm Xss-V2–18. The mutants were evaluated for pathogenicity in cotton based on symptomology and growth in planta. Four mutants showed attenuated virulence and all contained mutations in tal2. One tal2 mutant designated M2 was further investigated in complementation assays. When tal2 was introduced into Xcm M2 and expressed in trans, the mutant was complemented for both symptoms and growth in planta, thus indicating that tal2 functions as a virulence factor in Xcm Xss-V2–18. Conclusions Overall, the results demonstrated that Tal2 is a major pathogenicity factor in Xcm strain Xss-V2–18 that contributes significantly in BBC. This study provides a foundation for future efforts aimed at identifying susceptibility genes in cotton that are targeted by Tal2.
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Affiliation(s)
- Fazal Haq
- School of Agriculture and Biology, Shanghai Jiao Tong University/Key Laboratory of Urban Agriculture by the Ministry of Agriculture, Shanghai, 200240, China.,State Key laboratory of Microbial Metabolism, School of life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Shiwang Xie
- School of Agriculture and Biology, Shanghai Jiao Tong University/Key Laboratory of Urban Agriculture by the Ministry of Agriculture, Shanghai, 200240, China
| | - Kunxuan Huang
- School of Agriculture and Biology, Shanghai Jiao Tong University/Key Laboratory of Urban Agriculture by the Ministry of Agriculture, Shanghai, 200240, China.,State Key laboratory of Microbial Metabolism, School of life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Syed Mashab Ali Shah
- School of Agriculture and Biology, Shanghai Jiao Tong University/Key Laboratory of Urban Agriculture by the Ministry of Agriculture, Shanghai, 200240, China.,State Key laboratory of Microbial Metabolism, School of life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wenxiu Ma
- School of Agriculture and Biology, Shanghai Jiao Tong University/Key Laboratory of Urban Agriculture by the Ministry of Agriculture, Shanghai, 200240, China.,State Key laboratory of Microbial Metabolism, School of life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Lulu Cai
- School of Agriculture and Biology, Shanghai Jiao Tong University/Key Laboratory of Urban Agriculture by the Ministry of Agriculture, Shanghai, 200240, China.,State Key laboratory of Microbial Metabolism, School of life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiameng Xu
- School of Agriculture and Biology, Shanghai Jiao Tong University/Key Laboratory of Urban Agriculture by the Ministry of Agriculture, Shanghai, 200240, China.,State Key laboratory of Microbial Metabolism, School of life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Zhengyin Xu
- School of Agriculture and Biology, Shanghai Jiao Tong University/Key Laboratory of Urban Agriculture by the Ministry of Agriculture, Shanghai, 200240, China.,State Key laboratory of Microbial Metabolism, School of life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Sai Wang
- School of Agriculture and Biology, Shanghai Jiao Tong University/Key Laboratory of Urban Agriculture by the Ministry of Agriculture, Shanghai, 200240, China
| | - Lifang Zou
- School of Agriculture and Biology, Shanghai Jiao Tong University/Key Laboratory of Urban Agriculture by the Ministry of Agriculture, Shanghai, 200240, China.,State Key laboratory of Microbial Metabolism, School of life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Bo Zhu
- School of Agriculture and Biology, Shanghai Jiao Tong University/Key Laboratory of Urban Agriculture by the Ministry of Agriculture, Shanghai, 200240, China
| | - Gongyou Chen
- School of Agriculture and Biology, Shanghai Jiao Tong University/Key Laboratory of Urban Agriculture by the Ministry of Agriculture, Shanghai, 200240, China. .,State Key laboratory of Microbial Metabolism, School of life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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19
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Quibod IL, Atieza-Grande G, Oreiro EG, Palmos D, Nguyen MH, Coronejo ST, Aung EE, Nugroho C, Roman-Reyna V, Burgos MR, Capistrano P, Dossa SG, Onaga G, Saloma C, Cruz CV, Oliva R. The Green Revolution shaped the population structure of the rice pathogen Xanthomonas oryzae pv. oryzae. THE ISME JOURNAL 2020; 14:492-505. [PMID: 31666657 PMCID: PMC6976662 DOI: 10.1038/s41396-019-0545-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 10/15/2019] [Accepted: 10/17/2019] [Indexed: 11/15/2022]
Abstract
The impact of modern agriculture on the evolutionary trajectory of plant pathogens is a central question for crop sustainability. The Green Revolution replaced traditional rice landraces with high-yielding varieties, creating a uniform selection pressure that allows measuring the effect of such intervention. In this study, we analyzed a unique historical pathogen record to assess the impact of a major resistance gene, Xa4, in the population structure of Xanthomonas oryzae pv. oryzae (Xoo) collected in the Philippines in a span of 40 years. After the deployment of Xa4 in the early 1960s, the emergence of virulent pathogen groups was associated with the increasing adoption of rice varieties carrying Xa4, which reached 80% of the total planted area. Whole genomes analysis of a representative sample suggested six major pathogen groups with distinctive signatures of selection in genes related to secretion system, cell-wall degradation, lipopolysaccharide production, and detoxification of host defense components. Association genetics also suggested that each population might evolve different mechanisms to adapt to Xa4. Interestingly, we found evidence of strong selective sweep affecting several populations in the mid-1980s, suggesting a major bottleneck that coincides with the peak of Xa4 deployment in the archipelago. Our study highlights how modern agricultural practices facilitate the adaptation of pathogens to overcome the effects of standard crop improvement efforts.
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Affiliation(s)
- Ian Lorenzo Quibod
- Rice Breeding Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Genelou Atieza-Grande
- Rice Breeding Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
- Institute of Weed Science, Entomology and Plant Pathology, College of Agriculture and Food Science, University of the Philippines, Los Baños, Philippines
| | - Eula Gems Oreiro
- Rice Breeding Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Denice Palmos
- Philippine Genome Center, National Science Complex, University of the Philippines, Diliman, 1101, Quezon City, Philippines
| | - Marian Hanna Nguyen
- Rice Breeding Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Sapphire Thea Coronejo
- Rice Breeding Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Ei Ei Aung
- Rice Breeding Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Cipto Nugroho
- Rice Breeding Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
- Assessment Institute for Agricultural Technology Southeast Sulawesi, Indonesian Agency for Agricultural Research and Development, Jl. M. Yamin No. 89 Puwatu, Kendari, 93114, Indonesia
| | - Veronica Roman-Reyna
- Rice Breeding Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Maria Ruby Burgos
- Rice Breeding Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Pauline Capistrano
- Rice Breeding Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Sylvestre G Dossa
- Rice Breeding Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
- Food and Agriculture Organization of the United Nations, Immeuble Bel Espace-Batterie IV, Libreville, Gabon
| | - Geoffrey Onaga
- Rice Breeding Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Cynthia Saloma
- Philippine Genome Center, National Science Complex, University of the Philippines, Diliman, 1101, Quezon City, Philippines
| | - Casiana Vera Cruz
- Rice Breeding Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Ricardo Oliva
- Rice Breeding Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines.
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20
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Tekete C, Cunnac S, Doucouré H, Dembele M, Keita I, Sarra S, Dagno K, Koita O, Verdier V. Characterization of New Races of Xanthomonas oryzae pv. oryzae in Mali Informs Resistance Gene Deployment. PHYTOPATHOLOGY 2020; 110:267-277. [PMID: 31464159 DOI: 10.1094/phyto-02-19-0070-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Bacterial leaf blight caused by Xanthomonas oryzae pv. oryzae represents a severe threat to rice cultivation in Mali. Characterizing the pathotypic diversity of bacterial populations is key to the management of pathogen-resistant varieties. Forty-one X. oryzae pv. oryzae isolates were collected between 2010 and 2013 in the major rice growing regions in Mali. All isolates were virulent on the susceptible rice variety Azucena; evaluation of the isolates on 12 near isogenic rice lines, each carrying a single resistance gene, identified six new races (A4 to A9) and confirmed race A3 that was previously reported in Mali. Races A5 and A6, isolated in Office du Niger and Sélingué, were the most prevalent races in Mali. Race A9 was the most virulent, circumventing all of the resistance genes tested. Xa3 controlled six of seven races (i.e., 89% of the isolates tested). The expansion of race A9 represents a major risk to rice cultivation and highlights the urgent need to identify a local source of resistance. We selected 14 isolates of X. oryzae pv. oryzae representative of the most prevalent races to evaluate 29 rice varieties grown by farmers in Mali. Six isolates showed a high level of resistance to X. oryzae pv. oryzae and were then screened with a larger collection of isolates. Based on the interactions among the six varieties and the X. oryzae pv. oryzae isolates, we characterized eight different pathotypes (P1 to P8). Two rice varieties, SK20-28 and Gigante, effectively controlled all of the isolates tested. The low association observed among races and pathotypes of X. oryzae pv. oryzae suggests that the resistance observed in the local rice varieties does not simply rely on single known Xa genes. X. oryzae pv. oryzae is pathogenically and geographically diverse. Both the races of X. oryzae pv. oryzae characterized in this study and the identification of sources of resistance in local rice varieties provide useful information to inform the design of effective breeding programs for resistance to bacterial leaf blight in Mali.
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Affiliation(s)
- C Tekete
- Applied Molecular Biology Laboratory, Faculty of Science and Technology, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - S Cunnac
- IRD, CIRAD, University of Montpellier, IPME, Montpellier, France
| | - H Doucouré
- Applied Molecular Biology Laboratory, Faculty of Science and Technology, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - M Dembele
- Institute of Rural Economy, Regional Center for Agronomic Research, Niono and Bamako, Mali
| | - I Keita
- Applied Molecular Biology Laboratory, Faculty of Science and Technology, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - S Sarra
- Institute of Rural Economy, Regional Center for Agronomic Research, Niono and Bamako, Mali
| | - K Dagno
- Institute of Rural Economy, Regional Center for Agronomic Research, Niono and Bamako, Mali
| | - O Koita
- Applied Molecular Biology Laboratory, Faculty of Science and Technology, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - V Verdier
- IRD, CIRAD, University of Montpellier, IPME, Montpellier, France
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21
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Eom JS, Luo D, Atienza-Grande G, Yang J, Ji C, Thi Luu V, Huguet-Tapia JC, Char SN, Liu B, Nguyen H, Schmidt SM, Szurek B, Vera Cruz C, White FF, Oliva R, Yang B, Frommer WB. Diagnostic kit for rice blight resistance. Nat Biotechnol 2019; 37:1372-1379. [PMID: 31659338 PMCID: PMC6831515 DOI: 10.1038/s41587-019-0268-y] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 08/28/2019] [Indexed: 11/09/2022]
Abstract
Blight-resistant rice lines are the most effective solution for bacterial blight, caused by Xanthomonas oryzae pv. oryzae (Xoo). Key resistance mechanisms involve SWEET genes as susceptibility factors. Bacterial transcription activator-like (TAL) effectors bind to effector-binding elements (EBEs) in SWEET gene promoters and induce SWEET genes. EBE variants that cannot be recognized by TAL effectors abrogate induction, causing resistance. Here we describe a diagnostic kit to enable analysis of bacterial blight in the field and identification of suitable resistant lines. Specifically, we include a SWEET promoter database, RT–PCR primers for detecting SWEET induction, engineered reporter rice lines to visualize SWEET protein accumulation and knock-out rice lines to identify virulence mechanisms in bacterial isolates. We also developed CRISPR–Cas9 genome-edited Kitaake rice to evaluate the efficacy of EBE mutations in resistance, software to predict the optimal resistance gene set for a specific geographic region, and two resistant ‘mega’ rice lines that will empower farmers to plant lines that are most likely to resist rice blight. Strategic deployment of blight-resistant rice lines is enabled by a molecular diagnostic kit.
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Affiliation(s)
- Joon-Seob Eom
- Institute for Molecular Physiology and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University of Düsseldorf, Düsseldorf, Germany.,Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Dangping Luo
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Genelou Atienza-Grande
- International Rice Research Institute, Metro Manila, Philippines.,College of Agriculture and Food Science, University of the Philippines, Los Baños, Philippines
| | - Jungil Yang
- Institute for Molecular Physiology and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University of Düsseldorf, Düsseldorf, Germany.,Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Chonghui Ji
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Van Thi Luu
- Institute for Molecular Physiology and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University of Düsseldorf, Düsseldorf, Germany.,Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | | | - Si Nian Char
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA
| | - Bo Liu
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Hanna Nguyen
- International Rice Research Institute, Metro Manila, Philippines
| | - Sarah Maria Schmidt
- Institute for Molecular Physiology and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University of Düsseldorf, Düsseldorf, Germany.,Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Boris Szurek
- IRD, CIRAD, Université Montpellier, IPME, Montpellier, France
| | | | - Frank F White
- Department of Plant Pathology, University of Florida, Gainesville, FL, USA
| | - Ricardo Oliva
- International Rice Research Institute, Metro Manila, Philippines
| | - Bing Yang
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, USA. .,Donald Danforth Plant Science Center, St. Louis, MO, USA.
| | - Wolf B Frommer
- Institute for Molecular Physiology and Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University of Düsseldorf, Düsseldorf, Germany. .,Max Planck Institute for Plant Breeding Research, Cologne, Germany. .,Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Aichi, Japan.
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22
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Perez-Quintero AL, Szurek B. A Decade Decoded: Spies and Hackers in the History of TAL Effectors Research. ANNUAL REVIEW OF PHYTOPATHOLOGY 2019; 57:459-481. [PMID: 31387457 DOI: 10.1146/annurev-phyto-082718-100026] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Transcription activator-like effectors (TALEs) from the genus Xanthomonas are proteins with the remarkable ability to directly bind the promoters of genes in the plant host to induce their expression, which often helps bacterial colonization. Metaphorically, TALEs act as spies that infiltrate the plant disguised as high-ranking civilians (transcription factors) to trick the plant into activating weak points that allow an invasion. Current knowledge of how TALEs operate allows researchers to predict their activity (counterespionage) and exploit their function, engineering them to do our bidding (a Manchurian agent). This has been possible thanks particularly to the discovery of their DNA binding mechanism, which obeys specific amino acid-DNA correspondences (the TALE code). Here, we review the history of how researchers discovered the way these proteins work and what has changed in the ten years since the discovery of the code. Recommended music for reading this review can be found in the Supplemental Material.
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Affiliation(s)
- Alvaro L Perez-Quintero
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, Colorado 80523-1177, USA;
- IRD, CIRAD, Université Montpellier, IPME, 34000 Montpellier, France;
| | - Boris Szurek
- IRD, CIRAD, Université Montpellier, IPME, 34000 Montpellier, France;
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23
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Erkes A, Mücke S, Reschke M, Boch J, Grau J. PrediTALE: A novel model learned from quantitative data allows for new perspectives on TALE targeting. PLoS Comput Biol 2019; 15:e1007206. [PMID: 31295249 PMCID: PMC6650089 DOI: 10.1371/journal.pcbi.1007206] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 07/23/2019] [Accepted: 06/20/2019] [Indexed: 11/18/2022] Open
Abstract
Plant-pathogenic Xanthomonas bacteria secrete transcription activator-like effectors (TALEs) into host cells, where they act as transcriptional activators on plant target genes to support bacterial virulence. TALEs have a unique modular DNA-binding domain composed of tandem repeats. Two amino acids within each tandem repeat, termed repeat-variable diresidues, bind to contiguous nucleotides on the DNA sequence and determine target specificity. In this paper, we propose a novel approach for TALE target prediction to identify potential virulence targets. Our approach accounts for recent findings concerning TALE targeting, including frame-shift binding by repeats of aberrant lengths, and the flexible strand orientation of target boxes relative to the transcription start of the downstream target gene. The computational model can account for dependencies between adjacent RVD positions. Model parameters are learned from the wealth of quantitative data that have been generated over the last years. We benchmark the novel approach, termed PrediTALE, using RNA-seq data after Xanthomonas infection in rice, and find an overall improvement of prediction performance compared with previous approaches. Using PrediTALE, we are able to predict several novel putative virulence targets. However, we also observe that no target genes are predicted by any prediction tool for several TALEs, which we term orphan TALEs for this reason. We postulate that one explanation for orphan TALEs are incomplete gene annotations and, hence, propose to replace promoterome-wide by genome-wide scans for target boxes. We demonstrate that known targets from promoterome-wide scans may be recovered by genome-wide scans, whereas the latter, combined with RNA-seq data, are able to detect putative targets independent of existing gene annotations.
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Affiliation(s)
- Annett Erkes
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Stefanie Mücke
- Department of Plant Biotechnology, Leibniz Universität Hannover, Hannover, Germany
| | - Maik Reschke
- Department of Plant Biotechnology, Leibniz Universität Hannover, Hannover, Germany
| | - Jens Boch
- Department of Plant Biotechnology, Leibniz Universität Hannover, Hannover, Germany
| | - Jan Grau
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle, Germany
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24
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Lang JM, Pérez-Quintero AL, Koebnik R, DuCharme E, Sarra S, Doucoure H, Keita I, Ziegle J, Jacobs JM, Oliva R, Koita O, Szurek B, Verdier V, Leach JE. A Pathovar of Xanthomonas oryzae Infecting Wild Grasses Provides Insight Into the Evolution of Pathogenicity in Rice Agroecosystems. FRONTIERS IN PLANT SCIENCE 2019; 10:507. [PMID: 31114597 PMCID: PMC6503118 DOI: 10.3389/fpls.2019.00507] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 04/02/2019] [Indexed: 05/21/2023]
Abstract
Xanthomonas oryzae (Xo) are globally important rice pathogens. Virulent lineages from Africa and Asia and less virulent strains from the United States have been well characterized. Xanthomonas campestris pv. leersiae (Xcl), first described in 1957, causes bacterial streak on the perennial grass, Leersia hexandra, and is a close relative of Xo. L. hexandra, a member of the Poaceae, is highly similar to rice phylogenetically, is globally ubiquitous around rice paddies, and is a reservoir of pathogenic Xo. We used long read, single molecule real time (SMRT) genome sequences of five strains of Xcl from Burkina Faso, China, Mali, and Uganda to determine the genetic relatedness of this organism with Xo. Novel transcription activator-like effectors (TALEs) were discovered in all five strains of Xcl. Predicted TALE target sequences were identified in the Leersia perrieri genome and compared to rice susceptibility gene homologs. Pathogenicity screening on L. hexandra and diverse rice cultivars confirmed that Xcl are able to colonize rice and produce weak but not progressive symptoms. Overall, based on average nucleotide identity (ANI), type III (T3) effector repertoires, and disease phenotype, we propose to rename Xcl to X. oryzae pv. leersiae (Xol) and use this parallel system to improve understanding of the evolution of bacterial pathogenicity in rice agroecosystems.
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Affiliation(s)
- Jillian M. Lang
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, United States
- IRD, Cirad, Univ. Montpellier, IPME, Montpellier, France
| | - Alvaro L. Pérez-Quintero
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, United States
- IRD, Cirad, Univ. Montpellier, IPME, Montpellier, France
| | - Ralf Koebnik
- IRD, Cirad, Univ. Montpellier, IPME, Montpellier, France
| | - Elysa DuCharme
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, United States
| | - Soungalo Sarra
- Centre Régional de Recherche Agronomique de Niono, Institut d’Economie Rural, Bamako, Mali
| | - Hinda Doucoure
- Laboratoire de Biologie Moléculaire Appliquée, Université des Sciences Techniques et Technologiques de Bamako, Bamako, Mali
| | - Ibrahim Keita
- Laboratoire de Biologie Moléculaire Appliquée, Université des Sciences Techniques et Technologiques de Bamako, Bamako, Mali
| | - Janet Ziegle
- Pacific Biosciences, Menlo Park, CA, United States
| | - Jonathan M. Jacobs
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, United States
- IRD, Cirad, Univ. Montpellier, IPME, Montpellier, France
- Department of Plant Pathology, Infectious Disease Institute, Ohio State University, Columbus, OH, United States
| | - Ricardo Oliva
- International Rice Research Institute, Los Baños, Philippines
| | - Ousmane Koita
- Laboratoire de Biologie Moléculaire Appliquée, Université des Sciences Techniques et Technologiques de Bamako, Bamako, Mali
| | - Boris Szurek
- IRD, Cirad, Univ. Montpellier, IPME, Montpellier, France
| | - Valérie Verdier
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, United States
- IRD, Cirad, Univ. Montpellier, IPME, Montpellier, France
| | - Jan E. Leach
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, United States
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25
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Mücke S, Reschke M, Erkes A, Schwietzer CA, Becker S, Streubel J, Morgan RD, Wilson GG, Grau J, Boch J. Transcriptional Reprogramming of Rice Cells by Xanthomonas oryzae TALEs. FRONTIERS IN PLANT SCIENCE 2019; 10:162. [PMID: 30858855 PMCID: PMC6397873 DOI: 10.3389/fpls.2019.00162] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 01/29/2019] [Indexed: 05/12/2023]
Abstract
Rice-pathogenic Xanthomonas oryzae bacteria cause severe harvest loss and challenge a stable food supply. The pathogen virulence relies strongly on bacterial TALE (transcription activator-like effector) proteins that function as transcriptional activators inside the plant cell. To understand the plant targets of TALEs, we determined the genome sequences of the Indian X. oryzae pv. oryzae (Xoo) type strain ICMP 3125T and the strain PXO142 from the Philippines. Their complete TALE repertoire was analyzed and genome-wide TALE targets in rice were characterized. Integrating computational target predictions and rice transcriptomics data, we were able to verify 12 specifically induced target rice genes. The TALEs of the Xoo strains were reconstructed and expressed in a TALE-free Xoo strain to attribute specific induced genes to individual TALEs. Using reporter assays, we could show that individual TALEs act directly on their target promoters. In particular, we show that TALE classes assigned by AnnoTALE reflect common target genes, and that TALE classes of Xoo and the related pathogen X. oryzae pv. oryzicola share more common target genes than previously believed. Taken together, we establish a detailed picture of TALE-induced plant processes that significantly expands our understanding of X. oryzae virulence strategies and will facilitate the development of novel resistances to overcome this important rice disease.
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Affiliation(s)
- Stefanie Mücke
- Department of Plant Biotechnology, Institute of Plant Genetics, Leibniz Universität Hannover, Hanover, Germany
| | - Maik Reschke
- Department of Plant Biotechnology, Institute of Plant Genetics, Leibniz Universität Hannover, Hanover, Germany
| | - Annett Erkes
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Claudia-Alice Schwietzer
- Department of Plant Biotechnology, Institute of Plant Genetics, Leibniz Universität Hannover, Hanover, Germany
| | - Sebastian Becker
- Department of Plant Biotechnology, Institute of Plant Genetics, Leibniz Universität Hannover, Hanover, Germany
| | - Jana Streubel
- Department of Plant Biotechnology, Institute of Plant Genetics, Leibniz Universität Hannover, Hanover, Germany
| | | | | | - Jan Grau
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Jens Boch
- Department of Plant Biotechnology, Institute of Plant Genetics, Leibniz Universität Hannover, Hanover, Germany
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26
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Chien CC, Chou MY, Chen CY, Shih MC. Analysis of genetic diversity of Xanthomonas oryzae pv. oryzae populations in Taiwan. Sci Rep 2019; 9:316. [PMID: 30670790 PMCID: PMC6342995 DOI: 10.1038/s41598-018-36575-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 11/25/2018] [Indexed: 01/22/2023] Open
Abstract
Rice bacterial blight caused by Xanthomonas oryzae pv. oryzae (Xoo) is a major rice disease. In Taiwan, the tropical indica type of Oryza sativa originally grown in this area is mix-cultivated with the temperate japonica type of O. sativa, and this might have led to adaptive changes of both rice host and Xoo isolates. In order to better understand how Xoo adapts to this unique environment, we collected and analyzed fifty-one Xoo isolates in Taiwan. Three different genetic marker systems consistently identified five groups. Among these groups, two of them had unique sequences in the last acquired ten spacers in the clustered regularly interspaced short palindromic repeats (CRISPR) region, and the other two had sequences that were similar to the Japanese isolate MAFF311018 and the Philippines isolate PXO563, respectively. The genomes of two Taiwanese isolates with unique CRISPR sequence features, XF89b and XM9, were further completely sequenced. Comparison of the genome sequences suggested that XF89b is phylogenetically close to MAFF311018, and XM9 is close to PXO563. Here, documentation of the diversity of groups of Xoo in Taiwan provides evidence of the populations from different sources and hitherto missing information regarding distribution of Xoo populations in East Asia.
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Affiliation(s)
- Chih-Cheng Chien
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 115, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 115, Taiwan
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, 402, Taiwan
| | - Mei-Yi Chou
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Chun-Yi Chen
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 115, Taiwan
- Bioinformatics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 115, Taiwan
- Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan
| | - Ming-Che Shih
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 115, Taiwan.
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 115, Taiwan.
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, 402, Taiwan.
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27
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Carpenter SCD, Mishra P, Ghoshal C, Dash PK, Wang L, Midha S, Laha GS, Lore JS, Kositratana W, Singh NK, Singh K, Patil PB, Oliva R, Patarapuwadol S, Bogdanove AJ, Rai R. A Strain of an Emerging Indian Xanthomonas oryzae pv. oryzae Pathotype Defeats the Rice Bacterial Blight Resistance Gene xa13 Without Inducing a Clade III SWEET Gene and Is Nearly Identical to a Recent Thai Isolate. Front Microbiol 2018; 9:2703. [PMID: 30483230 PMCID: PMC6243107 DOI: 10.3389/fmicb.2018.02703] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 10/23/2018] [Indexed: 01/03/2023] Open
Abstract
The rice bacterial blight pathogen Xanthomonas oryzae pv. oryzae (Xoo) injects transcription activator-like effectors (TALEs) that bind and activate host "susceptibility" (S) genes important for disease. Clade III SWEET genes are major S genes for bacterial blight. The resistance genes xa5, which reduces TALE activity generally, and xa13, a SWEET11 allele not recognized by the cognate TALE, have been effectively deployed. However, strains that defeat both resistance genes individually were recently reported in India and Thailand. To gain insight into the mechanism(s), we completely sequenced the genome of one such strain from each country and examined the encoded TALEs. Strikingly, the two strains are clones, sharing nearly identical TALE repertoires, including a TALE known to activate SWEET11 strongly enough to be effective even when diminished by xa5. We next investigated SWEET gene induction by the Indian strain. The Indian strain induced no clade III SWEET in plants harboring xa13, indicating a pathogen adaptation that relieves dependence on these genes for susceptibility. The findings open a door to mechanistic understanding of the role SWEET genes play in susceptibility and illustrate the importance of complete genome sequence-based monitoring of Xoo populations in developing varieties with effective disease resistance.
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Affiliation(s)
- Sara C. D. Carpenter
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Prashant Mishra
- Plant Pathogen Interaction, National Research Centre on Plant Biotechnology (ICAR), New Delhi, India
| | - Chandrika Ghoshal
- Plant Pathogen Interaction, National Research Centre on Plant Biotechnology (ICAR), New Delhi, India
| | - Prasanta K. Dash
- Plant Pathogen Interaction, National Research Centre on Plant Biotechnology (ICAR), New Delhi, India
| | - Li Wang
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Samriti Midha
- Bacterial Genomics and Evolution Laboratory, Institute of Microbial Technology (CSIR), Chandigarh, India
| | - Gouri S. Laha
- Department of Plant Pathology, Indian Institute of Rice Research (ICAR), Hyderabad, India
| | - Jagjeet S. Lore
- Department of Plant Pathology, Punjab Agricultural University, Ludhiana, India
| | - Wichai Kositratana
- Department of Plant Pathology, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom, Thailand
| | - Nagendra K. Singh
- Plant Pathogen Interaction, National Research Centre on Plant Biotechnology (ICAR), New Delhi, India
| | - Kuldeep Singh
- National Bureau of Plant Genetic Resources (ICAR), New Delhi, India
| | - Prabhu B. Patil
- Bacterial Genomics and Evolution Laboratory, Institute of Microbial Technology (CSIR), Chandigarh, India
| | - Ricardo Oliva
- Rice Breeding Platform, International Rice Research Institute, Los Banos, Philippines
| | - Sujin Patarapuwadol
- Department of Plant Pathology, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom, Thailand
| | - Adam J. Bogdanove
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Rhitu Rai
- Plant Pathogen Interaction, National Research Centre on Plant Biotechnology (ICAR), New Delhi, India
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28
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Rice Routes of Countering Xanthomonas oryzae. Int J Mol Sci 2018; 19:ijms19103008. [PMID: 30279356 PMCID: PMC6213470 DOI: 10.3390/ijms19103008] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 09/26/2018] [Accepted: 09/29/2018] [Indexed: 12/02/2022] Open
Abstract
Bacterial blight (BB) and bacterial leaf streak (BLS), caused by Xanthomonas oryzae pv. oryzae and Xanthomonas oryzae pv. oryzicola, respectively, are two devastating diseases in rice planting areas worldwide. It has been proven that adoption of rice resistance is the most effective, economic, and environment-friendly strategy to avoid yield loss caused by BB and BLS. As a model system for plant—pathogen interaction, the rice—X. oryzae pathosystem has been intensively investigated in the past decade. Abundant studies have shown that the resistance and susceptibility of rice to X. oryzae is determined by molecular interactions between rice genes or their products and various pathogen effectors. In this review, we briefly overviewed the literature regarding the diverse interactions, focusing on recent advances in uncovering mechanisms of rice resistance and X. oryzae virulence. Our analysis and discussions will not only be helpful for getting a better understanding of coevolution of the rice innate immunity and X. oryzae virulence, but it will also provide new insights for application of plant R genes in crop breeding.
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29
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Zaka A, Grande G, Coronejo T, Quibod IL, Chen CW, Chang SJ, Szurek B, Arif M, Cruz CV, Oliva R. Natural variations in the promoter of OsSWEET13 and OsSWEET14 expand the range of resistance against Xanthomonas oryzae pv. oryzae. PLoS One 2018; 13:e0203711. [PMID: 30212546 PMCID: PMC6136755 DOI: 10.1371/journal.pone.0203711] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 08/24/2018] [Indexed: 01/21/2023] Open
Abstract
Bacterial blight, caused by Xanthomonas oryzae pv. oryzae (Xoo), is one of the major diseases that impact rice production in Asia. The bacteria use transcription activator-like effectors (TALEs) to hijack the host transcription machinery and activate key susceptibility (S) genes, specifically members of the SWEET sucrose uniporters through the recognition of effector-binding element (EBEs) in the promoter regions. However, natural variations in the EBEs that alter the binding affinity of TALEs usually prevent sufficient induction of SWEET genes, leading to resistance phenotypes. In this study, we identified candidate resistance alleles by mining a rice diversity panel for mutations in the promoter of OsSWEET13 and OsSWEET14, which are direct targets of three major TALEs PthXo2, PthXo3 and AvrXa7. We found natural variations at the EBE of both genes, which appeared to have emerged independently in at least three rice subspecies. For OsSWEET13, a 2-bp deletion at the 5th and 6th positions of the EBE, and a substitution at the 17th position appear to be sufficient to prevent activation by PthXo2. Similarly, a single nucleotide substitution at position 10 compromised the induction of OsSWEET14 by AvrXa7. These findings might increase our opportunities to reduce pathogen virulence by preventing the induction of SWEET transporters. Pyramiding variants along with other resistance genes may provide durable and broad-spectrum resistance to the disease.
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Affiliation(s)
- Abha Zaka
- Agriculture Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang road, Faisalabad, Punjab, Pakistan
- Department of Biological Sciences, Pakistan Institute of Engineering and Applied Sciences (PIEAS), P.O. Nilore, Islamabad, Punjab, Pakistan
| | - Genelou Grande
- Rice Breeding Platform, International Rice Research Institute, Metro Manila, Philippines
| | - Thea Coronejo
- Rice Breeding Platform, International Rice Research Institute, Metro Manila, Philippines
| | - Ian Lorenzo Quibod
- Rice Breeding Platform, International Rice Research Institute, Metro Manila, Philippines
| | - Chun-Wei Chen
- Taiwan Agricultural Research Institute, Agricultural Research and Extension Station, Council of Agriculture, Guannan, Miaoli District, Taiwan
| | - Su-Jein Chang
- Taiwan Agricultural Research Institute, Agricultural Research and Extension Station, Council of Agriculture, Guannan, Miaoli District, Taiwan
| | - Boris Szurek
- IRD, CIRAD, Université Montpellier, IPME, Montpellier, France
| | - Muhammad Arif
- Agriculture Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang road, Faisalabad, Punjab, Pakistan
- Department of Biological Sciences, Pakistan Institute of Engineering and Applied Sciences (PIEAS), P.O. Nilore, Islamabad, Punjab, Pakistan
| | - Casiana Vera Cruz
- Rice Breeding Platform, International Rice Research Institute, Metro Manila, Philippines
| | - Ricardo Oliva
- Rice Breeding Platform, International Rice Research Institute, Metro Manila, Philippines
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30
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Doucouré H, Pérez-Quintero AL, Reshetnyak G, Tekete C, Auguy F, Thomas E, Koebnik R, Szurek B, Koita O, Verdier V, Cunnac S. Functional and Genome Sequence-Driven Characterization of tal Effector Gene Repertoires Reveals Novel Variants With Altered Specificities in Closely Related Malian Xanthomonas oryzae pv. oryzae Strains. Front Microbiol 2018; 9:1657. [PMID: 30127769 PMCID: PMC6088199 DOI: 10.3389/fmicb.2018.01657] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 07/03/2018] [Indexed: 11/13/2022] Open
Abstract
Rice bacterial leaf blight (BLB) is caused by Xanthomonas oryzae pv. oryzae (Xoo) which injects Transcription Activator-Like Effectors (TALEs) into the host cell to modulate the expression of target disease susceptibility genes. Xoo major-virulence TALEs universally target susceptibility genes of the SWEET sugar transporter family. TALE-unresponsive alleles of OsSWEET genes have been identified in the rice germplasm or created by genome editing and confer resistance to BLB. In recent years, BLB has become one of the major biotic constraints to rice cultivation in Mali. To inform the deployment of alternative sources of resistance in this country, rice lines carrying alleles of OsSWEET14 unresponsive to either TalF (formerly Tal5) or TalC, two important TALEs previously identified in West African Xoo, were challenged with a panel of strains recently isolated in Mali and were found to remain susceptible to these isolates. The characterization of TALE repertoires revealed that talF and talC specific molecular markers were simultaneously present in all surveyed Malian strains, suggesting that the corresponding TALEs are broadly deployed by Malian Xoo to redundantly target the OsSWEET14 gene promoter. Consistent with this, the capacity of most Malian Xoo to induce OsSWEET14 was unaffected by either talC- or talF-unresponsive alleles of this gene. Long-read sequencing and assembly of eight Malian Xoo genomes confirmed the widespread occurrence of active TalF and TalC variants and provided a detailed insight into the diversity of TALE repertoires. All sequenced strains shared nine evolutionary related tal effector genes. Notably, a new TalF variant that is unable to induce OsSWEET14 was identified. Furthermore, two distinct TalB variants were shown to have lost the ability to simultaneously induce two susceptibility genes as previously reported for the founding members of this group from strains MAI1 and BAI3. Yet, both new TalB variants retained the ability to induce one or the other of the two susceptibility genes. These results reveal molecular and functional differences in tal repertoires and will be important for the sustainable deployment of broad-spectrum and durable resistance to BLB in West Africa.
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Affiliation(s)
- Hinda Doucouré
- IRD, Cirad, Université de Montpellier, IPME, Montpellier, France
- Laboratoire de Biologie Moléculaire Appliquée, Faculté des Sciences et Techniques, Université des Sciences Techniques et Technologiques de Bamako, Bamako, Mali
| | | | - Ganna Reshetnyak
- IRD, Cirad, Université de Montpellier, IPME, Montpellier, France
| | - Cheick Tekete
- IRD, Cirad, Université de Montpellier, IPME, Montpellier, France
- Laboratoire de Biologie Moléculaire Appliquée, Faculté des Sciences et Techniques, Université des Sciences Techniques et Technologiques de Bamako, Bamako, Mali
| | - Florence Auguy
- IRD, Cirad, Université de Montpellier, IPME, Montpellier, France
| | - Emilie Thomas
- IRD, Cirad, Université de Montpellier, IPME, Montpellier, France
| | - Ralf Koebnik
- IRD, Cirad, Université de Montpellier, IPME, Montpellier, France
| | - Boris Szurek
- IRD, Cirad, Université de Montpellier, IPME, Montpellier, France
| | - Ousmane Koita
- Laboratoire de Biologie Moléculaire Appliquée, Faculté des Sciences et Techniques, Université des Sciences Techniques et Technologiques de Bamako, Bamako, Mali
| | - Valérie Verdier
- IRD, Cirad, Université de Montpellier, IPME, Montpellier, France
| | - Sébastien Cunnac
- IRD, Cirad, Université de Montpellier, IPME, Montpellier, France
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31
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Functional analysis of African Xanthomonas oryzae pv. oryzae TALomes reveals a new susceptibility gene in bacterial leaf blight of rice. PLoS Pathog 2018; 14:e1007092. [PMID: 29864161 PMCID: PMC6037387 DOI: 10.1371/journal.ppat.1007092] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Revised: 07/09/2018] [Accepted: 05/12/2018] [Indexed: 11/19/2022] Open
Abstract
Most Xanthomonas species translocate Transcription Activator-Like (TAL) effectors into plant cells where they function like plant transcription factors via a programmable DNA-binding domain. Characterized strains of rice pathogenic X. oryzae pv. oryzae harbor 9–16 different tal effector genes, but the function of only a few of them has been decoded. Using sequencing of entire genomes, we first performed comparative analyses of the complete repertoires of TAL effectors, herein referred to as TALomes, in three Xoo strains forming an African genetic lineage different from Asian Xoo. A phylogenetic analysis of the three TALomes combined with in silico predictions of TAL effector targets showed that African Xoo TALomes are highly conserved, genetically distant from Asian ones, and closely related to TAL effectors from the bacterial leaf streak pathogen Xanthomonas oryzae pv. oryzicola (Xoc). Nine clusters of TAL effectors could be identified among the three TALomes, including three showing higher levels of variation in their repeat variable diresidues (RVDs). Detailed analyses of these groups revealed recombination events as a possible source of variation among TAL effector genes. Next, to address contribution to virulence, nine TAL effector genes from the Malian Xoo strain MAI1 and four allelic variants from the Burkinabe Xoo strain BAI3, thus representing most of the TAL effector diversity in African Xoo strains, were expressed in the TAL effector-deficient X. oryzae strain X11-5A for gain-of-function assays. Inoculation of the susceptible rice variety Azucena lead to the discovery of three TAL effectors promoting virulence, including two TAL effectors previously reported to target the susceptibility (S) gene OsSWEET14 and a novel major virulence contributor, TalB. RNA profiling experiments in rice and in silico prediction of EBEs were carried out to identify candidate targets of TalB, revealing OsTFX1, a bZIP transcription factor previously identified as a bacterial blight S gene, and OsERF#123, which encodes a subgroup IXc AP2/ERF transcription factor. Use of designer TAL effectors demonstrated that induction of either gene resulted in greater susceptibility to strain X11-5A. The induction of OsERF#123 by BAI3Δ1, a talB knockout derivative of BAI3, carrying these designer TAL effectors increased virulence of BAI3Δ1, validating OsERF#123 as a new, bacterial blight S gene. The ability of most Xanthomonas plant pathogenic bacteria to infect their hosts relies on the action of a specific family of proteins called TAL effectors, which are transcriptional activators injected into the plant by the bacteria. TAL effectors enter the plant cell nucleus and bind to the promoters of specific plant genes. Genes that when induced can benefit pathogen multiplication or disease development are called susceptibility (S) genes. Here, we perform a comparative analysis of the TAL effector repertoires of three strains of X. oryzae pv. oryzae, which causes bacterial leaf blight of rice, a major yield constraint in this staple crop. Using sequencing of entire genomes, we compared the large repertoires of TAL effectors in three African Xoo strains which form a genetic lineage distinct from Asian strains. We assessed the individual contribution to pathogen virulence of 13 TAL effector variants represented in the three strains, and identified one that makes a major contribution. By combining host transcriptome profiling and TAL effector binding sites prediction, we identified two targets of this TAL effector that function as S genes, one previously identified, and one, new S gene. We validated the new S gene by functional characterization using designer TAL effectors. Both S genes encode transcription factors and can therefore be considered as susceptibility hubs for pathogen manipulation of the host transcriptome. Our results provide new insights into the diversified strategies underlying the roles of TAL effectors in promoting plant disease.
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32
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Erkes A, Reschke M, Boch J, Grau J. Evolution of Transcription Activator-Like Effectors in Xanthomonas oryzae. Genome Biol Evol 2018. [PMID: 28637323 PMCID: PMC5512977 DOI: 10.1093/gbe/evx108] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Transcription activator-like effectors (TALEs) are secreted by plant–pathogenic Xanthomonas bacteria into plant cells where they act as transcriptional activators and, hence, are major drivers in reprogramming the plant for the benefit of the pathogen. TALEs possess a highly repetitive DNA-binding domain of typically 34 amino acid (AA) tandem repeats, where AA 12 and 13, termed repeat variable di-residue (RVD), determine target specificity. Different Xanthomonas strains possess different repertoires of TALEs. Here, we study the evolution of TALEs from the level of RVDs determining target specificity down to the level of DNA sequence with focus on rice-pathogenic Xanthomonas oryzae pv. oryzae (Xoo) and Xanthomonas oryzae pv. oryzicola (Xoc) strains. We observe that codon pairs coding for individual RVDs are conserved to a similar degree as the flanking repeat sequence. We find strong indications that TALEs may evolve 1) by base substitutions in codon pairs coding for RVDs, 2) by recombination of N-terminal or C-terminal regions of existing TALEs, or 3) by deletion of individual TALE repeats, and we propose possible mechanisms. We find indications that the reassortment of TALE genes in clusters is mediated by an integron-like mechanism in Xoc. We finally study the effect of the presence/absence and evolutionary modifications of TALEs on transcriptional activation of putative target genes in rice, and find that even single RVD swaps may lead to considerable differences in activation. This correlation allowed a refined prediction of TALE targets, which is the crucial step to decipher their virulence activity.
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Affiliation(s)
- Annett Erkes
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Maik Reschke
- Department of Plant Biotechnology, Leibniz Universität Hannover, Germany
| | - Jens Boch
- Department of Plant Biotechnology, Leibniz Universität Hannover, Germany
| | - Jan Grau
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
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33
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Pérez-Quintero AL, Lamy L, Zarate CA, Cunnac S, Doyle E, Bogdanove A, Szurek B, Dereeper A. daTALbase: A Database for Genomic and Transcriptomic Data Related to TAL Effectors. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:471-480. [PMID: 29143556 DOI: 10.1094/mpmi-06-17-0153-fi] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Transcription activator-like effectors (TALEs) are proteins found in the genus Xanthomonas of phytopathogenic bacteria. These proteins enter the nucleus of cells in the host plant and can induce the expression of susceptibility genes (S genes), triggering disease. TALEs bind the promoter region of S genes following a specific code, which allows the prediction of binding sites based on TALEs amino acid sequences. New candidate S genes can then be discovered by finding the intersection between genes induced in the presence of TALEs and genes containing predicted effector binding elements. By contrasting differential expression data and binding site predictions across different datasets, patterns of TALE diversification or convergence may be unveiled, but this requires the seamless integration of different genomic and transcriptomic data. With this in mind, we present daTALbase, a curated relational database that integrates TALE-related data including bacterial TALE sequences, plant promoter sequences, predicted TALE binding sites, transcriptomic data of host plants in response to TALE-harboring bacteria, and other associated data. The database can be explored to uncover new candidate S genes as well as to study variation in TALE repertories and their corresponding targets. The first version of the database here presented includes data for Oryza sp.-Xanthomonas pv. oryzae interactions. Future versions of the database will incorporate information for other pathosystems involving TALEs.
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Affiliation(s)
- Alvaro L Pérez-Quintero
- 1 IRD, Cirad, Université Montpellier, IPME, Montpellier (34000), France
- 2 Institut de Biologie de l'Ecole Normale Supérieure, Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, 75005 Paris, France
| | - Léo Lamy
- 1 IRD, Cirad, Université Montpellier, IPME, Montpellier (34000), France
| | - Carlos A Zarate
- 1 IRD, Cirad, Université Montpellier, IPME, Montpellier (34000), France
| | - Sébastien Cunnac
- 1 IRD, Cirad, Université Montpellier, IPME, Montpellier (34000), France
| | - Erin Doyle
- 3 Department of Biology, Doane University, 1014 Boswell Avenue, Crete, NE 68333, U.S.A.; and
| | - Adam Bogdanove
- 3 Department of Biology, Doane University, 1014 Boswell Avenue, Crete, NE 68333, U.S.A.; and
- 4 Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, 334 Plant Science Building, Ithaca, NY 14853, U.S.A
| | - Boris Szurek
- 1 IRD, Cirad, Université Montpellier, IPME, Montpellier (34000), France
| | - Alexis Dereeper
- 1 IRD, Cirad, Université Montpellier, IPME, Montpellier (34000), France
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34
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Dilla-Ermita CJ, Tandayu E, Juanillas VM, Detras J, Lozada DN, Dwiyanti MS, Vera Cruz C, Mbanjo EGN, Ardales E, Diaz MG, Mendioro M, Thomson MJ, Kretzschmar T. Genome-wide Association Analysis Tracks Bacterial Leaf Blight Resistance Loci In Rice Diverse Germplasm. RICE (NEW YORK, N.Y.) 2017; 10:8. [PMID: 28321828 PMCID: PMC5359197 DOI: 10.1186/s12284-017-0147-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 02/23/2017] [Indexed: 05/19/2023]
Abstract
BACKGROUND A range of resistance loci against different races of Xanthomonas oryzae pv. oryzae (Xoo), the pathogen causing bacterial blight (BB) disease of rice, have been discovered and characterized. Several have been deployed in modern varieties, however, due to rapid evolution of Xoo, a number have already become ineffective. The continuous "arms race" between Xoo and rice makes it imperative to discover new resistance loci to enable durable deployment of multiple resistance genes in modern breeding lines. Rice diversity panels can be exploited as reservoirs of useful genetic variation for bacterial blight (BB) resistance. This study was conducted to identify loci associated to BB resistance, new genetic donors and useful molecular markers for marker-assisted breeding. RESULTS A genome-wide association study (GWAS) of BB resistance using a diverse panel of 285 rice accessions was performed to identify loci that are associated with resistance to nine Xoo strains from the Philippines, representative of eight global races. Single nucleotide polymorphisms (SNPs) associated with differential resistance were identified in the diverse panel and a subset of 198 indica accessions. Strong associations were found for novel SNPs linked with known bacterial blight resistance Xa genes, from which high utility markers for tracking and selection of resistance genes in breeding programs were designed. Furthermore, significant associations of SNPs in chromosomes 6, 9, 11, and 12 did not overlap with known resistance loci and hence might prove to be novel sources of resistance. Detailed analysis revealed haplotypes that correlated with resistance and analysis of putative resistance alleles identified resistant genotypes as potential donors of new resistance genes. CONCLUSIONS The results of the GWAS validated known genes underlying resistance and identified novel loci that provide useful targets for further investigation. SNP markers and genetic donors identified in this study will help plant breeders in improving and diversifying resistance to BB.
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Affiliation(s)
- Christine Jade Dilla-Ermita
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Erwin Tandayu
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Venice Margarette Juanillas
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Jeffrey Detras
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Dennis Nicuh Lozada
- Crop, Soil, and Environmental Science, University of Arkansas, Fayettevile, AR, USA
| | - Maria Stefanie Dwiyanti
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Casiana Vera Cruz
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Edwige Gaby Nkouaya Mbanjo
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Edna Ardales
- Crop Protection Cluster, University of the Philippines Los Baños, College, Laguna, Philippines
| | - Maria Genaleen Diaz
- Institute of Biological Sciences, University of the Philippines Los Baños, College, Laguna, Philippines
| | - Merlyn Mendioro
- Institute of Biological Sciences, University of the Philippines Los Baños, College, Laguna, Philippines
| | - Michael J Thomson
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, USA
| | - Tobias Kretzschmar
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, Los Baños, Laguna, Philippines.
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35
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Nagel R, Turrini PCG, Nett RS, Leach JE, Verdier V, Van Sluys MA, Peters RJ. An operon for production of bioactive gibberellin A 4 phytohormone with wide distribution in the bacterial rice leaf streak pathogen Xanthomonas oryzae pv. oryzicola. THE NEW PHYTOLOGIST 2017; 214:1260-1266. [PMID: 28134995 PMCID: PMC5388578 DOI: 10.1111/nph.14441] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 12/10/2016] [Indexed: 05/19/2023]
Abstract
Phytopathogens have developed elaborate mechanisms to attenuate the defense response of their host plants, including convergent evolution of complex pathways for production of the GA phytohormones, which were actually first isolated from the rice fungal pathogen Gibberella fujikuroi. The rice bacterial pathogen Xanthomonas oryzae pv. oryzicola (Xoc) has been demonstrated to contain a biosynthetic operon with cyclases capable of producing the universal GA precursor ent-kaurene. Genetic (knock-out) studies indicate that the derived diterpenoid serves as a virulence factor for this rice leaf streak pathogen, serving to reduce the jasmonic acid-mediated defense response. Here the functions of the remaining genes in the Xoc operon are elucidated and the distribution of the operon in X. oryzae is investigated in over 100 isolates. The Xoc operon leads to production of the bioactive GA4 , an additional step beyond production of the penultimate precursor GA9 mediated by the homologous operons recently characterized from rhizobia. Moreover, this GA biosynthetic operon was found to be widespread in Xoc (> 90%), but absent in the other major X. oryzae pathovar. These results indicate selective pressure for production of GA4 in the distinct lifestyle of Xoc, and the importance of GA to both fungal and bacterial pathogens of rice.
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Affiliation(s)
- Raimund Nagel
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Paula C. G. Turrini
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, São Paulo, Brasil
| | - Ryan S. Nett
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Jan E. Leach
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523, USA
| | - Valérie Verdier
- IRD – Cirad – Univ. Montpellier, UMR Interactions Plantes Microorganismes Environnement (IPME), 34399 Montpellier, France
| | - Marie-Anne Van Sluys
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, São Paulo, Brasil
| | - Reuben J. Peters
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
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McCann HC, Li L, Liu Y, Li D, Pan H, Zhong C, Rikkerink EH, Templeton MD, Straub C, Colombi E, Rainey PB, Huang H. Origin and Evolution of the Kiwifruit Canker Pandemic. Genome Biol Evol 2017; 9:932-944. [PMID: 28369338 PMCID: PMC5388287 DOI: 10.1093/gbe/evx055] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/13/2017] [Indexed: 12/18/2022] Open
Abstract
Recurring epidemics of kiwifruit (Actinidia spp.) bleeding canker disease are caused by Pseudomonas syringae pv. actinidiae (Psa). In order to strengthen understanding of population structure, phylogeography, and evolutionary dynamics, we isolated Pseudomonas from cultivated and wild kiwifruit across six provinces in China. Based on the analysis of 80 sequenced Psa genomes, we show that China is the origin of the pandemic lineage but that strain diversity in China is confined to just a single clade. In contrast, Korea and Japan harbor strains from multiple clades. Distinct independent transmission events marked introduction of the pandemic lineage into New Zealand, Chile, Europe, Korea, and Japan. Despite high similarity within the core genome and minimal impact of within-clade recombination, we observed extensive variation even within the single clade from which the global pandemic arose.
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Affiliation(s)
- Honour C. McCann
- New Zealand Institute for Advanced Study, Massey University, Auckland, New Zealand
| | - Li Li
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Yifei Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Dawei Li
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Hui Pan
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Caihong Zhong
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Erik H.A. Rikkerink
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Matthew D. Templeton
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
- School of Biological Sciences, University of Auckland, New Zealand
| | - Christina Straub
- New Zealand Institute for Advanced Study, Massey University, Auckland, New Zealand
| | - Elena Colombi
- New Zealand Institute for Advanced Study, Massey University, Auckland, New Zealand
| | - Paul B. Rainey
- New Zealand Institute for Advanced Study, Massey University, Auckland, New Zealand
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
- École Supérieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI ParisTech), CNRS UMR 8231 PSL Research University, Paris, France
| | - Hongwen Huang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
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